Abstract: Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process.

Abstract: The invention relates to a method of determining the T cell receptor ? chain (TRBC) gene type of a cell, the method comprising (a) determining the J gene type expressed in said cell, and (b) inferring from (a) the TRBC gene type expressed in said cell. The invention further relates to use of a CAR T cell targeted to a T cell receptor ? chain (TRBC) type 1, or a CAR T cell targeted to a T cell receptor ? chain (TRBC) type 2. The invention further relates to a method of medical treatment, and to nucleic acid probes.

Abstract: The invention relates to a method of pre-surgical risk stratification of a prostate cancer subject, comprising determining a gene expression profile for phosphodiesterase 4D variant 7 (PDE4D7) in a biological sample obtained from the subject, determining a gene expression profile for DExH-box helicase 9 (DHX9) in the same or another biological sample obtained from the subject, and determining a pre-surgical prognostic risk score for the subject based on the gene expression profile for PDE4D7 and the gene expression profile for DHX9. This may allow for an improved stratification of the subject in a pre-surgical setting that may result in better primary treatment decisions. For instance, the pre-surgical prognostic risk score may allow to make better recommendations on whether to select active surveillance vs. active intervention, e.g., radical prostatectomy, for certain sub-populations of prostate cancer patients.

Abstract: The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.

Abstract: The present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species. The present invention also provides a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

Abstract: Methods for quantifying DNA methylation that may be utilized for screening for diseases (e.g., cancer), diagnosing diseases (e.g., cancer type), monitoring progression of a disease, and monitoring response to a therapeutic treatment.

Abstract: Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and/or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.

Abstract: The invention generally relates to methods and compositions for the prediction of therapeutic efficacy of cancer treatments and the prognosis of cancer. The invention discloses markers that are associated with favorable and unfavorable outcomes, respectively, in certain cancer treatments and are useful as prognostic markers for cancer. Methods involving these markers are disclosed for predicting cancer therapy benefit and prognosing clinical outcome for cancer patients.

Abstract: Described herein are methods and compositions useful in detecting, diagnosing and treating small cell lung cancer. Transgenic animal models and cell lines are disclosed for the study of a small cell lung cancer subtype. Methods of screening and identifying active agents for the treatment of a small cell lung cancer subtype as well as methods of identifying patients susceptible to treatment with aurora kinase inhibitors are also provided.

Abstract: Disclosed is a method for determining the sex of yellowtails, the method comprising a step of identifying whether an amino acid residue at position 143 in polypeptide encoded by the HSD17B1 gene of yellowtails is a glutamic acid residue or a glycine residue; a nucleic acid molecule or a primer set which is for use in said method; or a kit comprising the same, for determining the sex of yellowtails. The method according to the present invention is useful in that the genetic sex of yellowtails can be accurately determined.

Abstract: The present invention provides oligonucleotides and methods for their use in the detection and/or differentiation of target nucleic acids. The oligonucleotides and methods find particular application in amplifying, detecting, and/or discriminating multiple targets simultaneously.

Abstract: The present invention provides methods for testing surgical fluid for biomarkers of disease, including cancer.

Abstract: A use of a detection reagent for a microRNA (miRNA) marker miR-143-3p in the preparation of a product for evaluating a therapeutic effect of olanzapine in the treatment of schizophrenia (SZ) and a kit are provided. An expression level of miR-143-3p can be detected to determine a therapeutic effect of olanzapine in the treatment of SZ of a patient, and can be used as a detection or treatment index in clinical practice, which provides a theoretical basis for the mechanism research of SZ and the clinical application.

Abstract: Biomarkers and methods for identifying circulating serum-based cfDNA sequences. The cfDNA sequences (PDcRAs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.

Abstract: Nucleic acids and proteins having a mutant C-RAF sequence, and methods of identifying patients having cancer who are likely to benefit from a combination therapy and methods of treatment are provided.

Abstract: Methods and compositions are provided for determining a subtype of lung squamous cell carcinoma (SQ) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung squamous cell carcinoma. Also provided herein are methods and compositions for determining the response of an individual with a squamous cell carcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy such as immunotherapy.

Abstract: The present application provides an in vitro method for determining the degradation of the extracellular matrix (ECM) in a subject, the method comprising determining in an isolated sample from the subject the level of an expression product of at least one gene selected from the group consisting of collagen type V alpha 1 chain (COL5A1), transforming growth factor beta-1 (TGFB1), integrin subunit alpha 4 (ITGA4), integrin subunit beta 1 (ITGB1), matrix metallopeptidase 2 (MMP2), matrix metallopeptidase 9 (MMP9) and bone morphogenetic protein 1 (BMP1), the at least one gene being determined optionally in combination with one or both of collagen type XI alpha 1 chain (COL11A1) and collagen type V alpha 2 chain (COL5A2), wherein when the level of the expression product(s) is(are) higher than a reference value this is indicative of a degraded ECM. Methods for the diagnosis and prognosis of cancer and aneurysms are also provided.

Abstract: The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.

Abstract: Methods for diagnosing propensity to exhibit acquired peripheral neuropathy in dogs are described. The methods and kits test dogs for presence of a disease-associated genomic variant. Presence of the genomic variant indicates an increased likelihood of the dog developing an acquired peripheral neuropathy. This information can be used to guide preemptive clinical treatment of the animal for peripheral neuropathy and to choose dogs for selective breeding programs.